A Middlesex FA investigation into the club's financial affairs necessitated a change to professional status mid-season, but a forgettable campaign ended with the Bees finishing third-from-bottom.
[1] Brentford won and drew each of the opening two Second Division fixtures, with new forward John Bayne scoring in each, before he and George Turner, both soldiers, departed for service in the Second Boer War with their regiments.
[1] Things went from bad to worse in October when the Middlesex FA opened an enquiry into Brentford's "shamateurism", the results of which saw the club fined £10 and suspended from football for a month beginning 20 November.
[1] Following the resumption of competitive play on 23 December, Brentford showed appalling form, failing to win until late March 1900.
[2] Additionally, a meeting had been called in January to discuss if the club could even continue, but donations of £60 (equivalent to £8,500 in 2025) helped to ensure that the Bees would survive for the immediate future.